deploy: phasorpy/phasorpy@02c3f81

main/_downloads/2a87616bb17ef75a216689cb0c820281/phasorpy_introduction.py

@@ -160,12 +160,9 @@
 # Applying median filter to the calibrated phasor coordinates,
 # often multiple times, improves contrast:
 
-# TODO: replace this with a ``phasor_filter`` function?
-from skimage.filters import median
+from phasorpy.phasor import phasor_filter
 
-for _ in range(2):
-    real = median(real)
-    imag = median(imag)
+real, imag = phasor_filter(real, imag, method='median', size=3, repeat=2)
 
 # %%
 # Pixels with low intensities are commonly excluded from analysis and

main/_downloads/519fde79147cf545361411cda356f9f9/phasorpy_introduction.ipynb

@@ -191,7 +191,7 @@
       },
       "outputs": [],
       "source": [
-        "# TODO: replace this with a ``phasor_filter`` function?\nfrom skimage.filters import median\n\nfor _ in range(2):\n    real = median(real)\n    imag = median(imag)"
+        "from phasorpy.phasor import phasor_filter\n\nreal, imag = phasor_filter(real, imag, method='median', size=3, repeat=2)"
       ]
     },
     {

main/_sources/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:28.853** total execution time for 9 files **from all galleries**:
+**00:25.749** total execution time for 9 files **from all galleries**:
 
 .. container::
 
@@ -33,28 +33,28 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_tutorials_phasorpy_introduction.py` (``../tutorials/phasorpy_introduction.py``)
-     - 00:11.479
+     - 00:08.742
      - 0.0
    * - :ref:`sphx_glr_tutorials_benchmarks_phasorpy_phasor_from_signal.py` (``../tutorials/benchmarks/phasorpy_phasor_from_signal.py``)
-     - 00:07.622
+     - 00:07.593
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_components.py` (``../tutorials/phasorpy_components.py``)
-     - 00:05.377
+     - 00:05.283
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_fret.py` (``../tutorials/phasorpy_fret.py``)
      - 00:01.729
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_cursors.py` (``../tutorials/phasorpy_cursors.py``)
-     - 00:01.270
+     - 00:01.013
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_phasorplot.py` (``../tutorials/phasorpy_phasorplot.py``)
-     - 00:00.695
+     - 00:00.699
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_phasor_from_lifetime.py` (``../tutorials/phasorpy_phasor_from_lifetime.py``)
-     - 00:00.439
+     - 00:00.454
      - 0.0
    * - :ref:`sphx_glr_tutorials_phasorpy_pca.py` (``../tutorials/phasorpy_pca.py``)
-     - 00:00.193
+     - 00:00.188
      - 0.0
    * - :ref:`sphx_glr_tutorials_misc_phasorpy_logo.py` (``../tutorials/misc/phasorpy_logo.py``)
      - 00:00.049

main/_sources/tutorials/benchmarks/phasorpy_phasor_from_signal.rst.txt

@@ -148,35 +148,35 @@ and number of threads:
     harmonics 1
       axis -1
         phasor_from_signal       0.057s   1.00
-          threads 2              0.031s   0.54
-        phasor_from_signal_fft   0.217s   3.82
-          scipy_fft              0.232s   4.08
+          threads 2              0.031s   0.55
+        phasor_from_signal_fft   0.220s   3.86
+          scipy_fft              0.236s   4.14
       axis 0
-        phasor_from_signal       0.164s   2.89
-          threads 2              0.080s   1.41
-        phasor_from_signal_fft   0.451s   7.94
-          scipy_fft              0.346s   6.10
+        phasor_from_signal       0.164s   2.88
+          threads 2              0.080s   1.40
+        phasor_from_signal_fft   0.452s   7.95
+          scipy_fft              0.346s   6.09
       axis 2
         phasor_from_signal       0.057s   1.00
           threads 2              0.031s   0.55
-        phasor_from_signal_fft   0.215s   3.79
-          scipy_fft              0.233s   4.11
+        phasor_from_signal_fft   0.218s   3.83
+          scipy_fft              0.234s   4.11
     harmonics 8
       axis -1
-        phasor_from_signal       0.472s   8.31
-          threads 2              0.245s   4.32
-        phasor_from_signal_fft   0.230s   4.05
-          scipy_fft              0.244s   4.31
+        phasor_from_signal       0.455s   8.00
+          threads 2              0.248s   4.35
+        phasor_from_signal_fft   0.235s   4.13
+          scipy_fft              0.249s   4.38
       axis 0
-        phasor_from_signal       1.313s  23.13
-          threads 2              0.656s  11.56
-        phasor_from_signal_fft   0.457s   8.05
-          scipy_fft              0.352s   6.20
+        phasor_from_signal       1.307s  22.96
+          threads 2              0.653s  11.48
+        phasor_from_signal_fft   0.454s   7.98
+          scipy_fft              0.351s   6.17
       axis 2
-        phasor_from_signal       0.463s   8.15
-          threads 2              0.245s   4.32
-        phasor_from_signal_fft   0.228s   4.02
-          scipy_fft              0.245s   4.31
+        phasor_from_signal       0.456s   8.01
+          threads 2              0.244s   4.29
+        phasor_from_signal_fft   0.235s   4.13
+          scipy_fft              0.251s   4.40
 
 
 
@@ -254,7 +254,7 @@ when computing large number of harmonics with an optimized FFT function.
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 7.622 seconds)
+   **Total running time of the script:** (0 minutes 7.593 seconds)
 
 
 .. _sphx_glr_download_tutorials_benchmarks_phasorpy_phasor_from_signal.py:

main/_sources/tutorials/benchmarks/sg_execution_times.rst.txt

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:07.622** total execution time for 1 file **from tutorials/benchmarks**:
+**00:07.593** total execution time for 1 file **from tutorials/benchmarks**:
 
 .. container::
 
@@ -33,5 +33,5 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_tutorials_benchmarks_phasorpy_phasor_from_signal.py` (``phasorpy_phasor_from_signal.py``)
-     - 00:07.622
+     - 00:07.593
      - 0.0

main/_sources/tutorials/phasorpy_components.rst.txt

@@ -604,42 +604,42 @@ of components, A vs C and B vs C:
      </style>
 
      <div class="animation">
-       <img id="_anim_img7d5593deebf6474e83cd4651148e30cf">
+       <img id="_anim_img75902931552146ba862a7cd68ea69a31">
        <div class="anim-controls">
-         <input id="_anim_slider7d5593deebf6474e83cd4651148e30cf" type="range" class="anim-slider"
+         <input id="_anim_slider75902931552146ba862a7cd68ea69a31" type="range" class="anim-slider"
                 name="points" min="0" max="1" step="1" value="0"
-                oninput="anim7d5593deebf6474e83cd4651148e30cf.set_frame(parseInt(this.value));">
+                oninput="anim75902931552146ba862a7cd68ea69a31.set_frame(parseInt(this.value));">
          <div class="anim-buttons">
-           <button title="Decrease speed" aria-label="Decrease speed" onclick="anim7d5593deebf6474e83cd4651148e30cf.slower()">
+           <button title="Decrease speed" aria-label="Decrease speed" onclick="anim75902931552146ba862a7cd68ea69a31.slower()">
                <i class="fa fa-minus"></i></button>
-           <button title="First frame" aria-label="First frame" onclick="anim7d5593deebf6474e83cd4651148e30cf.first_frame()">
+           <button title="First frame" aria-label="First frame" onclick="anim75902931552146ba862a7cd68ea69a31.first_frame()">
              <i class="fa fa-fast-backward"></i></button>
-           <button title="Previous frame" aria-label="Previous frame" onclick="anim7d5593deebf6474e83cd4651148e30cf.previous_frame()">
+           <button title="Previous frame" aria-label="Previous frame" onclick="anim75902931552146ba862a7cd68ea69a31.previous_frame()">
                <i class="fa fa-step-backward"></i></button>
-           <button title="Play backwards" aria-label="Play backwards" onclick="anim7d5593deebf6474e83cd4651148e30cf.reverse_animation()">
+           <button title="Play backwards" aria-label="Play backwards" onclick="anim75902931552146ba862a7cd68ea69a31.reverse_animation()">
                <i class="fa fa-play fa-flip-horizontal"></i></button>
-           <button title="Pause" aria-label="Pause" onclick="anim7d5593deebf6474e83cd4651148e30cf.pause_animation()">
+           <button title="Pause" aria-label="Pause" onclick="anim75902931552146ba862a7cd68ea69a31.pause_animation()">
                <i class="fa fa-pause"></i></button>
-           <button title="Play" aria-label="Play" onclick="anim7d5593deebf6474e83cd4651148e30cf.play_animation()">
+           <button title="Play" aria-label="Play" onclick="anim75902931552146ba862a7cd68ea69a31.play_animation()">
                <i class="fa fa-play"></i></button>
-           <button title="Next frame" aria-label="Next frame" onclick="anim7d5593deebf6474e83cd4651148e30cf.next_frame()">
+           <button title="Next frame" aria-label="Next frame" onclick="anim75902931552146ba862a7cd68ea69a31.next_frame()">
                <i class="fa fa-step-forward"></i></button>
-           <button title="Last frame" aria-label="Last frame" onclick="anim7d5593deebf6474e83cd4651148e30cf.last_frame()">
+           <button title="Last frame" aria-label="Last frame" onclick="anim75902931552146ba862a7cd68ea69a31.last_frame()">
                <i class="fa fa-fast-forward"></i></button>
-           <button title="Increase speed" aria-label="Increase speed" onclick="anim7d5593deebf6474e83cd4651148e30cf.faster()">
+           <button title="Increase speed" aria-label="Increase speed" onclick="anim75902931552146ba862a7cd68ea69a31.faster()">
                <i class="fa fa-plus"></i></button>
          </div>
-         <form title="Repetition mode" aria-label="Repetition mode" action="#n" name="_anim_loop_select7d5593deebf6474e83cd4651148e30cf"
+         <form title="Repetition mode" aria-label="Repetition mode" action="#n" name="_anim_loop_select75902931552146ba862a7cd68ea69a31"
                class="anim-state">
-           <input type="radio" name="state" value="once" id="_anim_radio1_7d5593deebf6474e83cd4651148e30cf"
+           <input type="radio" name="state" value="once" id="_anim_radio1_75902931552146ba862a7cd68ea69a31"
                   >
-           <label for="_anim_radio1_7d5593deebf6474e83cd4651148e30cf">Once</label>
-           <input type="radio" name="state" value="loop" id="_anim_radio2_7d5593deebf6474e83cd4651148e30cf"
+           <label for="_anim_radio1_75902931552146ba862a7cd68ea69a31">Once</label>
+           <input type="radio" name="state" value="loop" id="_anim_radio2_75902931552146ba862a7cd68ea69a31"
                   checked>
-           <label for="_anim_radio2_7d5593deebf6474e83cd4651148e30cf">Loop</label>
-           <input type="radio" name="state" value="reflect" id="_anim_radio3_7d5593deebf6474e83cd4651148e30cf"
+           <label for="_anim_radio2_75902931552146ba862a7cd68ea69a31">Loop</label>
+           <input type="radio" name="state" value="reflect" id="_anim_radio3_75902931552146ba862a7cd68ea69a31"
                   >
-           <label for="_anim_radio3_7d5593deebf6474e83cd4651148e30cf">Reflect</label>
+           <label for="_anim_radio3_75902931552146ba862a7cd68ea69a31">Reflect</label>
          </form>
        </div>
      </div>
@@ -649,9 +649,9 @@ of components, A vs C and B vs C:
        /* Instantiate the Animation class. */
        /* The IDs given should match those used in the template above. */
        (function() {
-         var img_id = "_anim_img7d5593deebf6474e83cd4651148e30cf";
-         var slider_id = "_anim_slider7d5593deebf6474e83cd4651148e30cf";
-         var loop_select_id = "_anim_loop_select7d5593deebf6474e83cd4651148e30cf";
+         var img_id = "_anim_img75902931552146ba862a7cd68ea69a31";
+         var slider_id = "_anim_slider75902931552146ba862a7cd68ea69a31";
+         var loop_select_id = "_anim_loop_select75902931552146ba862a7cd68ea69a31";
          var frames = new Array(20);
 
        frames[0] = "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAiQAAAMgCAYAAAATFXnSAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90\
@@ -16461,7 +16461,7 @@ of components, A vs C and B vs C:
          /* set a timeout to make sure all the above elements are created before
             the object is initialized. */
          setTimeout(function() {
-             anim7d5593deebf6474e83cd4651148e30cf = new Animation(frames, img_id, slider_id, 100.0,
+             anim75902931552146ba862a7cd68ea69a31 = new Animation(frames, img_id, slider_id, 100.0,
                                       loop_select_id);
          }, 0);
        })()
@@ -16480,7 +16480,7 @@ mypy: disable-error-code="arg-type"
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 5.377 seconds)
+   **Total running time of the script:** (0 minutes 5.283 seconds)
 
 
 .. _sphx_glr_download_tutorials_phasorpy_components.py:

main/_sources/tutorials/phasorpy_cursors.rst.txt

@@ -357,7 +357,7 @@ sphinx_gallery_thumbnail_number = 1
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 1.270 seconds)
+   **Total running time of the script:** (0 minutes 1.013 seconds)
 
 
 .. _sphx_glr_download_tutorials_phasorpy_cursors.py:

main/_sources/tutorials/phasorpy_introduction.rst.txt

@@ -318,17 +318,14 @@ Filter phasor coordinates
 Applying median filter to the calibrated phasor coordinates,
 often multiple times, improves contrast:
 
-.. GENERATED FROM PYTHON SOURCE LINES 162-170
+.. GENERATED FROM PYTHON SOURCE LINES 162-167
 
 .. code-block:: Python
 
 
-    # TODO: replace this with a ``phasor_filter`` function?
-    from skimage.filters import median
+    from phasorpy.phasor import phasor_filter
 
-    for _ in range(2):
-        real = median(real)
-        imag = median(imag)
+    real, imag = phasor_filter(real, imag, method='median', size=3, repeat=2)
 
 
 
@@ -337,12 +334,12 @@ often multiple times, improves contrast:
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 171-173
+.. GENERATED FROM PYTHON SOURCE LINES 168-170
 
 Pixels with low intensities are commonly excluded from analysis and
 visualization of phasor coordinates:
 
-.. GENERATED FROM PYTHON SOURCE LINES 173-179
+.. GENERATED FROM PYTHON SOURCE LINES 170-176
 
 .. code-block:: Python
 
@@ -359,7 +356,7 @@ visualization of phasor coordinates:
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 180-188
+.. GENERATED FROM PYTHON SOURCE LINES 177-185
 
 Plot phasor coordinates
 -----------------------
@@ -370,7 +367,7 @@ plotting phasor and polar coordinates.
 Large number of phasor coordinates, such as obtained from imaging,
 are commonly visualized as 2D histograms:
 
-.. GENERATED FROM PYTHON SOURCE LINES 188-197
+.. GENERATED FROM PYTHON SOURCE LINES 185-194
 
 .. code-block:: Python
 
@@ -395,11 +392,11 @@ are commonly visualized as 2D histograms:
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 198-199
+.. GENERATED FROM PYTHON SOURCE LINES 195-196
 
 For comparison, the uncalibrated, unfiltered phasor coordinates:
 
-.. GENERATED FROM PYTHON SOURCE LINES 199-205
+.. GENERATED FROM PYTHON SOURCE LINES 196-202
 
 .. code-block:: Python
 
@@ -421,19 +418,19 @@ For comparison, the uncalibrated, unfiltered phasor coordinates:
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 206-208
+.. GENERATED FROM PYTHON SOURCE LINES 203-205
 
 To be continued
 ---------------
 
-.. GENERATED FROM PYTHON SOURCE LINES 210-214
+.. GENERATED FROM PYTHON SOURCE LINES 207-211
 
 Appendix
 --------
 
 Print information about Python interpreter and installed packages:
 
-.. GENERATED FROM PYTHON SOURCE LINES 214-217
+.. GENERATED FROM PYTHON SOURCE LINES 211-214
 
 .. code-block:: Python
 
@@ -468,14 +465,14 @@ Print information about Python interpreter and installed packages:
 
 
 
-.. GENERATED FROM PYTHON SOURCE LINES 218-219
+.. GENERATED FROM PYTHON SOURCE LINES 215-216
 
 sphinx_gallery_thumbnail_number = 3
 
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 11.479 seconds)
+   **Total running time of the script:** (0 minutes 8.742 seconds)
 
 
 .. _sphx_glr_download_tutorials_phasorpy_introduction.py:

main/_sources/tutorials/phasorpy_pca.rst.txt

@@ -253,7 +253,7 @@ sphinx_gallery_thumbnail_number = -2
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.193 seconds)
+   **Total running time of the script:** (0 minutes 0.188 seconds)
 
 
 .. _sphx_glr_download_tutorials_phasorpy_pca.py:

main/_sources/tutorials/phasorpy_phasor_from_lifetime.rst.txt

@@ -359,7 +359,7 @@ sphinx_gallery_thumbnail_number = -2
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.439 seconds)
+   **Total running time of the script:** (0 minutes 0.454 seconds)
 
 
 .. _sphx_glr_download_tutorials_phasorpy_phasor_from_lifetime.py:

main/_sources/tutorials/phasorpy_phasorplot.rst.txt

@@ -490,7 +490,7 @@ sphinx_gallery_thumbnail_number = 10
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** (0 minutes 0.695 seconds)
+   **Total running time of the script:** (0 minutes 0.699 seconds)
 
 
 .. _sphx_glr_download_tutorials_phasorpy_phasorplot.py: